Trigger and Oddjob thanks. The way I had mounted them before was pretty close and good enough to have a good working exhaust. I can't recall if I made a mistake when I mounted my (2nd) set many years ago or that I have copied the way I found the old (1st) set mounted. Intrigued by Sohron's description I decided to investigate. I guess what has happened is this. The brackets are somewhat forgiving and torqueing the 10 mm bolt that goes through the footpeg accomodated a good working exhaust by bending the bracket of the lower pipe (mistakenly mounted on the outside) somewhat. Now, where a 10 mm bolt can easily do that, I can't expect the rubber connecting tube to undo it and bend it back. So the irony is that in spite I have them now mounted correctly, due to the way I had mounted them before, it is harder to align the balance tubes than before. Anyway, I think I stay with how I've mounted them now and live with the not fully aligned balance tubes. Although the looks before were not bad, seen from the front it now even looks better.
Interesting is that when I finally had the old copper gaskets out, I could clearly see they had been making good overall contact and had sealed well. It is true the headers showed some more discoloration (looks nice btw) than my first set did, but gasoline has changed too and I ride my bike pretty hot.